Remove any markers for which all founders, in the study, are homozygous for the wild-type allele. Since we do not model de novo mutations, it is not possible for non-founders to develop mutations at these loci.
remove_allWild(f_haps, SNV_map)The founder haplotypes data. This is a list of family lists. By family, this contains the haplotypes for each founder (first item), and a list of ID numbers (second item) which is used to map the haplotype to the person to whom it belongs.
data.frame. Catalogs the SNV data contained in the familial haplotypes.
A list (by family) of haplotype matrices and ID vectors and the reduce marker data set.